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- EMDB-51870: Escherichia phage Paracelsus (Bas36) baseplate, proximal tail fib... -

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Basic information

Entry
Database: EMDB / ID: EMD-51870
TitleEscherichia phage Paracelsus (Bas36) baseplate, proximal tail fiber and tail.
Map dataBas36 baseplate, tail, and proximal LTF C6 map
Sample
  • Virus: Escherichia phage EmilHeitz (virus)
KeywordsBaseplate / Tail fiber / Tail tube / Tail sheath / VIRUS
Biological speciesEscherichia phage EmilHeitz (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsKlein-Sousa V / Roa-Eguiara A / Taylor NMI
Funding support Denmark, 5 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17OC0031006 Denmark
Novo Nordisk FoundationNNF23OC0081528 Denmark
Novo Nordisk FoundationNNF21OC0071948 Denmark
Novo Nordisk FoundationNNF0069780 Denmark
CitationJournal: Sci Adv / Year: 2025
Title: RBPseg: Toward a complete phage tail fiber structure atlas.
Authors: Victor Klein-Sousa / Aritz Roa-Eguiara / Claudia S Kielkopf / Nicholas Sofos / Nicholas M I Taylor /
Abstract: Bacteriophages use receptor-binding proteins (RBPs) to adhere to bacterial hosts, yet their sequence and structural diversity remain poorly understood. Tail fibers, a major class of RBPs, are ...Bacteriophages use receptor-binding proteins (RBPs) to adhere to bacterial hosts, yet their sequence and structural diversity remain poorly understood. Tail fibers, a major class of RBPs, are elongated and flexible trimeric proteins, making their full-length structures difficult to resolve experimentally. Advances in deep learning-based protein structure prediction, such as AlphaFold2-multimer (AF2M) and ESMFold, provide opportunities for studying these challenging proteins. Here, we introduce RBPseg, a method that combines monomeric ESMFold predictions with a structural-based domain identification approach, to divide tail fiber sequences into manageable fractions for high-confidence modeling with AF2M. Using this approach, we generated complete tail fiber models, validated by single-particle cryo-electron microscopy of five fibers from three phages. A structural classification of 67 fibers identified 16 distinct classes and 89 domains, revealing patterns of modularity, convergence, divergence, and domain swapping. Our findings suggest that these structural classes represent at least 24% of the known tail fiber universe, providing key insights into their evolution and functionality.
History
DepositionOct 22, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51870.png

Downloads & links

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Map

FileDownload / File: emd_51870.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBas36 baseplate, tail, and proximal LTF C6 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.62 Å/pix.
x 208 pix.
= 960. Å		4.62 Å/pix.
x 208 pix.
= 960. Å		4.62 Å/pix.
x 208 pix.
= 960. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.61538 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.3351424 - 4.301544
Average (Standard dev.)-0.0021864318 (±0.26257807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 960.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51870_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C1 Local refinement map of proximal LTF

Fileemd_51870_additional_1.map
AnnotationC1 Local refinement map of proximal LTF
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map

Fileemd_51870_half_map_1.map
AnnotationHalf A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map

Fileemd_51870_half_map_2.map
AnnotationHalf B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage EmilHeitz

EntireName: Escherichia phage EmilHeitz (virus)
Components
  • Virus: Escherichia phage EmilHeitz (virus)

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Supramolecule #1: Escherichia phage EmilHeitz

SupramoleculeName: Escherichia phage EmilHeitz / type: virus / ID: 1 / Parent: 0
Details: Phage was amplified in liquid media by E. Coli MG1655 dRM infection, and purified using PEG precipitation and Opti-Prep Gradient.
NCBI-ID: 2852021 / Sci species name: Escherichia phage EmilHeitz / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
8.0 mMMgClmagnesium chloride
50.0 mMTris-HClTris hydrochloride
GridModel: UltrAuFoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: OTHER / Number images used: 7986
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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